trees_gene_groups: post-COPYME-restore doc audit — residual path + naming cleanup

Follow-up to 9595947 (other session: restored COPYME naming on 4 workflow
dirs + treated hugo_hgnc/snap_family as data via .gitignore-marker pattern).
That commit handled the dir renames and most path updates, but missed
some references in subproject-level docs and didn't catch
underscore-vs-hyphen typos in Where-this-fits sections (`gene_groups_COPYME`
should be `gene_groups-COPYME`).

This commit cleans up the residuals.

Fixed (16 files, all docs only — no code/config):

- Subproject README.md: workflow-{rbh_rbf_homologs,hgnc_database,hgnc_user_list}
  → workflow-COPYME-* (3 refs); removed obsolete "NOTE: STEP_1 + STEP_0 hgnc
  workflows currently lack the COPYME prefix" block (now fixed, note no
  longer applies).
- Subproject AI_GUIDE.md: workflow-hgnc_database / workflow-hgnc_user_list
  → workflow-COPYME-* (10 refs in Quick Reference table, dir tree, instance
  description, and Quick Start cmd snippets); fixed stale cross-ref
  AI_GUIDE-trees_gene_families.md → AI_GUIDE.md (was renamed in 61ef05a);
  annotated hugo_hgnc reference as gitignored-data-dir.
- gene_groups-COPYME/README.md: gene_groups_COPYME → gene_groups-COPYME
  (2 refs in cp/cd snippets + table); updated "Create AI_GUIDE-mysource.md"
  user-instruction → "Create AI_GUIDE.md (bare per §3)".
- 6 STEP-level AI_GUIDE.md `**Location**:` lines (3 per template):
  gene_groups_COPYME → gene_groups-COPYME.
- 5 workflow ai/AI_GUIDE.md `**Location**:` lines (3 in gene_groups-COPYME,
  2 in gene_groups_hgnc-COPYME): same.
- 4 PLAN-rgs_identification_improvements.md refs (2 in each template):
  gene_groups_COPYME → gene_groups-COPYME.
- Subproject AI_GUIDE.md: "Create AI_GUIDE-pfam.md" user-instruction →
  "Create gene_groups-pfam/AI_GUIDE.md (bare per §3)".

Out of scope this commit (left alone):
- gene_groups-hugo_hgnc/ and gene_groups-snap_family/ instance dirs:
  already correctly treated as data per 9595947 (only .gitignore tracked
  in each; all other contents untracked + gitignored).
- gene_groups-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/RUN-workflow.sh:
  unrelated unstaged modification predating this session — leaving for
  the responsible session to handle.
- Out-of-subproject deletions in ocl_perspectives/, ocl_using_simple_taxonomy/,
  parsimony_tree_structures/ — separate work, not staged here.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: 000specific

gigantic_project-COPYME/subprojects/trees_gene_groups/AI_GUIDE.md

@@ -44,15 +44,15 @@ Human:   Eric Edsinger
 | trees_gene_groups concepts (this file) | this file |
 | Generic (source-agnostic) template | `gene_groups-COPYME/README.md` |
 | HGNC-anchored template (newer, two STEP_0 modes) | `gene_groups_hgnc-COPYME/AI_GUIDE.md` |
-| HGNC source specifics (legacy instance) | `gene_groups-hugo_hgnc/AI_GUIDE-hugo_hgnc.md` |
+| HGNC source specifics (legacy instance) | `gene_groups-hugo_hgnc/AI_GUIDE-hugo_hgnc.md` (now in gitignored data dir; read on disk, not in git) |
 | Canonical HGNC reference data | `output_to_input/hugo_hgnc_database/README.md` |
 | STEP_1 concepts (RBH/RBF) | `gene_groups-COPYME/STEP_1-homolog_discovery/AI_GUIDE.md` |
 | STEP_2 concepts | `gene_groups-COPYME/STEP_2-phylogenetic_analysis/AI_GUIDE.md` |
 | STEP_3 concepts | `gene_groups-COPYME/STEP_3-tree_visualization/AI_GUIDE.md` |
-| HGNC STEP_0 (batch all HGNC groups) | `gene_groups_hgnc-COPYME/STEP_0-hgnc_based_rgs/workflow-hgnc_database/ai/AI_GUIDE.md` |
-| HGNC STEP_0 (ad-hoc user gene set) | `gene_groups_hgnc-COPYME/STEP_0-hgnc_based_rgs/workflow-hgnc_user_list/ai/AI_GUIDE.md` |
+| HGNC STEP_0 (batch all HGNC groups) | `gene_groups_hgnc-COPYME/STEP_0-hgnc_based_rgs/workflow-COPYME-hgnc_database/ai/AI_GUIDE.md` |
+| HGNC STEP_0 (ad-hoc user gene set) | `gene_groups_hgnc-COPYME/STEP_0-hgnc_based_rgs/workflow-COPYME-hgnc_user_list/ai/AI_GUIDE.md` |
 | Workflow execution details (STEP_1/2/3) | each `workflow-*/ai/AI_GUIDE-*.md` |
-| Shared RBH/RBF methodology with sister subproject | `../trees_gene_families/AI_GUIDE-trees_gene_families.md` |
+| Shared RBH/RBF methodology with sister subproject | `../trees_gene_families/AI_GUIDE.md` |
 
 ---
 
@@ -90,8 +90,8 @@ trees_gene_groups/
 ├── gene_groups_hgnc-COPYME/                               ← TEMPLATE 2: HGNC-anchored (NEW)
 │   ├── INPUT_user/user_gene_set_EXAMPLE.tsv               (for the user_list mode)
 │   ├── STEP_0-hgnc_based_rgs/                             (HGNC-specific)
-│   │   ├── workflow-hgnc_database/                        ← MODE 1: all HGNC groups
-│   │   └── workflow-hgnc_user_list/                       ← MODE 2: ad-hoc user set
+│   │   ├── workflow-COPYME-hgnc_database/                        ← MODE 1: all HGNC groups
+│   │   └── workflow-COPYME-hgnc_user_list/                       ← MODE 2: ad-hoc user set
 │   └── STEP_1, STEP_2, STEP_3                             (inherited from gene_groups-COPYME)
 │
 └── gene_groups-<instance>/                                ← INSTANCE: copy of one of the templates
@@ -121,7 +121,7 @@ Per-instance examples currently:
   Older code path; **kept as a research artifact**.
 - `gene_groups-snap_family/` — Synaptosomal-Associated Proteins
   (SNAP23/25/29/47); instance of `gene_groups_hgnc-COPYME` using the
-  `workflow-hgnc_user_list` mode.
+  `workflow-COPYME-hgnc_user_list` mode.
 
 ---
 
@@ -146,9 +146,9 @@ and Improvements 2–4 in script 008) was removed as dead code. RGS produced by
 either STEP_0 workflow always resolves cleanly via one of:
 
 - **Improvement 0** — strict gene-symbol search (4-field uniprot-sourced
-  RGS from `workflow-hgnc_user_list`)
+  RGS from `workflow-COPYME-hgnc_user_list`)
 - **Improvement 1** — exact NCBI accession match (5-field hgnc/ncbi-sourced
-  RGS from `workflow-hgnc_database`)
+  RGS from `workflow-COPYME-hgnc_database`)
 
 Both are strict and fail-fast. Forward + reciprocal BLAST against species70
 (the homolog discovery itself) is unchanged.
@@ -236,11 +236,11 @@ the common case.
 cp -r gene_groups_hgnc-COPYME gene_groups-<my_analysis>
 
 # 2a. Ad-hoc mode: edit INPUT_user/user_gene_set.tsv with your symbols
-#     Then: cd <instance>/STEP_0-hgnc_based_rgs/workflow-hgnc_user_list && bash RUN-workflow.sh
+#     Then: cd <instance>/STEP_0-hgnc_based_rgs/workflow-COPYME-hgnc_user_list && bash RUN-workflow.sh
 
-# 2b. Batch mode: edit STEP_0-hgnc_based_rgs/workflow-hgnc_database/START_HERE-user_config.yaml
+# 2b. Batch mode: edit STEP_0-hgnc_based_rgs/workflow-COPYME-hgnc_database/START_HERE-user_config.yaml
 #     to point at your human proteome.
-#     Then: cd <instance>/STEP_0-hgnc_based_rgs/workflow-hgnc_database && bash RUN-workflow.sh
+#     Then: cd <instance>/STEP_0-hgnc_based_rgs/workflow-COPYME-hgnc_database && bash RUN-workflow.sh
 
 # 3. Run STEP_1 → STEP_2 → STEP_3 from the same instance
 ```
@@ -261,7 +261,7 @@ mkdir -p gene_groups-pfam/STEP_0-pfam_clans/workflow-pfam_clans/
 #     STEP_0 must emit a per-group summary TSV (5-column) that STEP_1's
 #     orchestrator reads (see gene_groups_hgnc-COPYME's STEP_0 for the format).
 
-# 3. Create AI_GUIDE-pfam.md describing source specifics
+# 3. Create gene_groups-pfam/AI_GUIDE.md describing source specifics (bare AI_GUIDE.md per §3)
 
 # 4. Run STEP_0 → STEP_1 → STEP_2 → STEP_3
 ```

gigantic_project-COPYME/subprojects/trees_gene_groups/README.md

@@ -35,7 +35,7 @@ are hand-curated per family.
 | Path | Type | Purpose |
 |------|------|---------|
 | `gene_groups-COPYME/` | **Template (generic)** | Master pattern for non-HGNC sources. Has empty `STEP_0-placeholder/` for user to fill in source-specific RGS prep. Per §47 + memory `feedback_instance_naming_follows_template_prefix`, instances of THIS template are named `gene_groups-<source>/`. |
-| `gene_groups_hgnc-COPYME/` | **Template (HGNC-specialized)** | Master pattern for HGNC-derived sources, with concrete `STEP_0-hgnc_based_rgs/` containing two workflows: `workflow-hgnc_database/` (full HGNC download) and `workflow-hgnc_user_list/` (curated subset). Per §47 + the same naming memory, instances of THIS template are named `gene_groups_hgnc-<source>/`. |
+| `gene_groups_hgnc-COPYME/` | **Template (HGNC-specialized)** | Master pattern for HGNC-derived sources, with concrete `STEP_0-hgnc_based_rgs/` containing two workflows: `workflow-COPYME-hgnc_database/` (full HGNC download) and `workflow-COPYME-hgnc_user_list/` (curated subset). Per §47 + the same naming memory, instances of THIS template are named `gene_groups_hgnc-<source>/`. |
 | `gene_groups-hugo_hgnc/` | **FROZEN instance** | Older HGNC instance (~1,974 protein-coding groups) — predates `gene_groups_hgnc-COPYME`, uses its own pre-rework STEP_0 structure. Frozen per memory `feedback_research_instances_are_frozen_artifacts`. |
 | `gene_groups-snap_family/` | **FROZEN instance** | SNAP family experiment using newer STEP_0-hgnc_based_rgs layout. Frozen per the same rule. |
 | `output_to_input/` | Subproject output | Auto-populated by workflows |
@@ -48,7 +48,7 @@ are hand-curated per family.
 
 Both templates share STEPs 1-3; STEP_0 differs:
 - **Generic template** (`gene_groups-COPYME`): `STEP_0-placeholder/` — user fills in source-specific RGS prep
-- **HGNC template** (`gene_groups_hgnc-COPYME`): `STEP_0-hgnc_based_rgs/` with `workflow-hgnc_database/` + `workflow-hgnc_user_list/`
+- **HGNC template** (`gene_groups_hgnc-COPYME`): `STEP_0-hgnc_based_rgs/` with `workflow-COPYME-hgnc_database/` + `workflow-COPYME-hgnc_user_list/`
 
 | Step | Name | What |
 |------|------|------|
@@ -69,9 +69,6 @@ cp -r gene_groups_hgnc-COPYME gene_groups_hgnc-<your_source>
 # 2. Inside, for each STEP, copy the COPYME workflow to a RUN_N copy
 cd gene_groups_hgnc-<your_source>/STEP_1-homolog_discovery/
 cp -r workflow-COPYME-rbh_rbf_homologs workflow-RUN_1-rbh_rbf_homologs
-# NOTE: STEP_1 + STEP_0 hgnc workflows currently lack the COPYME prefix on disk
-# (workflow-rbh_rbf_homologs, workflow-hgnc_database, workflow-hgnc_user_list).
-# Pre-§3/§29 naming; deferred to a future rename pass.
 
 # 3. Edit RUN's config (execution_mode, paths, SLURM resources)
 cd workflow-RUN_1-rbh_rbf_homologs

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/README.md

@@ -51,15 +51,15 @@ gene_groups-COPYME/
 
 ```bash
 # 1. Copy the master template to a per-source instance
-cp -r gene_groups_COPYME gene_groups-mysource
+cp -r gene_groups-COPYME gene_groups-mysource
 
 # 2. Replace STEP_0-placeholder with source-specific RGS generation code
 rm -r gene_groups-mysource/STEP_0-placeholder/
 mkdir -p gene_groups-mysource/STEP_0-mysource/workflow-COPYME-mysource/
 # ... populate with the source's STEP_0 pipeline ...
 
 # 3. Per-source AI_GUIDE
-# Create gene_groups-mysource/AI_GUIDE-mysource.md describing source specifics
+# Create gene_groups-mysource/AI_GUIDE.md describing source specifics (bare AI_GUIDE.md per §3)
 
 # 4. Edit each STEP's START_HERE-user_config.yaml inside the per-source instance
 #    to point at the right STEP_0 output and pick execution_mode (local | slurm-standard | slurm-burst)
@@ -99,7 +99,7 @@ The `trees_gene_groups/` subproject has exactly two workflows:
 
 | Workflow | Purpose |
 |----------|---------|
-| `gene_groups_COPYME/` | This master template (never run from here) |
+| `gene_groups-COPYME/` | This master template (never run from here) |
 | `gene_groups-<source>/` | Per-source instance (copy of master + source-specific STEP_0) |
 
 To add a new source (Pfam, InterPro, custom): make another `gene_groups-<source>/`.

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_1-homolog_discovery/AI_GUIDE.md

@@ -23,7 +23,7 @@ Human:   Eric Edsinger
 
 **For AI Assistants**: Read `../../../AI_GUIDE.md` first for GIGANTIC overview. Then `../../AI_GUIDE.md` for subproject concepts. This guide covers STEP_1.
 
-**Location**: `gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups_COPYME/STEP_1-homolog_discovery/`
+**Location**: `gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_1-homolog_discovery/`
 
 ---
 

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_1-homolog_discovery/PLAN-rgs_identification_improvements.md

@@ -1,17 +1,17 @@
 # PLAN: Improve RGS Identification in Reference Proteomes
 
-**Status**: IMPLEMENTED in `gene_groups_COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/ai/scripts/008_ai-python-map_rgs_to_reference_genomes.py` (2026-05-24). Pending real-run verification on the next HGNC rerun.
+**Status**: IMPLEMENTED in `gene_groups-COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/ai/scripts/008_ai-python-map_rgs_to_reference_genomes.py` (2026-05-24). Pending real-run verification on the next HGNC rerun.
 **Original status**: Design — not yet implemented
 **Last updated**: 2026-05-24 (status); 2026-05-23 (content)
 **Author**: Eric Edsinger (with Claude Code, Opus 4.7)
-**Applies to**: `script 008_ai-python-map_rgs_to_reference_genomes.py` in `gene_groups_COPYME/.../workflow-COPYME-rbh_rbf_homologs/` (the canonical master for trees_gene_groups). The trees_gene_families version of script 008 follows the same design.
+**Applies to**: `script 008_ai-python-map_rgs_to_reference_genomes.py` in `gene_groups-COPYME/.../workflow-COPYME-rbh_rbf_homologs/` (the canonical master for trees_gene_groups). The trees_gene_families version of script 008 follows the same design.
 **Out of scope of this plan but related**: `RUN-update_upload_to_server.sh`, scripts 009/013, downstream re-runs.
 
 ---
 
 ## IMPLEMENTATION SUMMARY (2026-05-24)
 
-All 5 improvements have been implemented in the master `gene_groups_COPYME` script 008:
+All 5 improvements have been implemented in the master `gene_groups-COPYME` script 008:
 
 1. ✅ **NCBI accession match** — primary mechanism (deterministic for NCBI-sourced RGS)
 2. ✅ **Identity ≥95% AND symmetric coverage ≥95%** BLAST fallback with T1 length-invariant check
@@ -374,7 +374,7 @@ Recommended order — each phase is independently shippable:
 ## 11. Files affected (when implementing)
 
 ### Direct
-- `gene_groups_COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/ai/scripts/008_ai-python-map_rgs_to_reference_genomes.py` (rewrite of `create_rgs_genome_mapping` + new helper functions)
+- `gene_groups-COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/ai/scripts/008_ai-python-map_rgs_to_reference_genomes.py` (rewrite of `create_rgs_genome_mapping` + new helper functions)
 - `gene_family_COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/ai/scripts/008_ai-python-map_rgs_to_reference_genomes.py` (apply same changes — keep in sync)
 
 ### Indirect (may need updates depending on phase)
@@ -383,7 +383,7 @@ Recommended order — each phase is independently shippable:
 - `RUN-workflow.sh` — likely no change; the changes are inside Python only
 
 ### Downstream propagation (after master is fixed)
-- Per the master/instance pattern documented in [project_trees_gene_x_ags_rgs_duplication_bug](../../../../memory/project_trees_gene_x_ags_rgs_duplication_bug.md): after updating `gene_groups_COPYME/.../008` and `gene_family_COPYME/.../008`, propagate to:
+- Per the master/instance pattern documented in [project_trees_gene_x_ags_rgs_duplication_bug](../../../../memory/project_trees_gene_x_ags_rgs_duplication_bug.md): after updating `gene_groups-COPYME/.../008` and `gene_family_COPYME/.../008`, propagate to:
   - `gene_groups-<INSTANCE>/.../workflow-COPYME-rbh_rbf_homologs/ai/scripts/008` (downstream instance)
   - All 76 `trees_gene_families/gene_family-*/workflow-COPYME-rbh_rbf_homologs/ai/scripts/008` (downstream per-family instances)
   - Verify via md5sum that all 78 stay in sync after each phase

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/ai/AI_GUIDE.md

@@ -20,7 +20,7 @@ Human:   Eric Edsinger
 
 **For AI Assistants**: Read `../../AI_GUIDE.md` first for STEP_1 concepts. This guide covers workflow execution and orchestrator internals.
 
-**Location**: `gene_groups_COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/`
+**Location**: `gene_groups-COPYME/STEP_1-homolog_discovery/workflow-COPYME-rbh_rbf_homologs/`
 
 ---
 

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_2-phylogenetic_analysis/AI_GUIDE.md

@@ -22,7 +22,7 @@ Human:   Eric Edsinger
 
 **For AI Assistants**: Read `../../../AI_GUIDE.md` first for GIGANTIC overview. Then `../../AI_GUIDE.md` for subproject concepts. This guide covers STEP_2.
 
-**Location**: `gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups_COPYME/STEP_2-phylogenetic_analysis/`
+**Location**: `gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_2-phylogenetic_analysis/`
 
 ---
 

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_2-phylogenetic_analysis/workflow-COPYME-phylogenetic_analysis/ai/AI_GUIDE.md

@@ -18,7 +18,7 @@ Human:   Eric Edsinger
 
 **For AI Assistants**: Read `../../AI_GUIDE.md` first for STEP_2 concepts. This guide covers workflow execution.
 
-**Location**: `gene_groups_COPYME/STEP_2-phylogenetic_analysis/workflow-COPYME-phylogenetic_analysis/`
+**Location**: `gene_groups-COPYME/STEP_2-phylogenetic_analysis/workflow-COPYME-phylogenetic_analysis/`
 
 ---
 

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_3-tree_visualization/AI_GUIDE.md

@@ -21,7 +21,7 @@ Human:   Eric Edsinger
 
 **For AI Assistants**: Read `../../../AI_GUIDE.md` first for GIGANTIC overview. Then `../../AI_GUIDE.md` for subproject concepts. This guide covers STEP_3.
 
-**Location**: `gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups_COPYME/STEP_3-tree_visualization/`
+**Location**: `gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_3-tree_visualization/`
 
 ---
 

gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/AI_GUIDE.md

@@ -17,7 +17,7 @@ Human:   Eric Edsinger
 
 **For AI Assistants**: Read `../../AI_GUIDE.md` first for STEP_3 concepts. This guide covers workflow execution.
 
-**Location**: `gene_groups_COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/`
+**Location**: `gene_groups-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/`
 
 ---